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Conserved domains on  [gi|12323218|gb|AAG51590|]
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unknown protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 13329789)

pentatricopeptide repeat (PPR)-containing protein may form anti-parallel alpha helices and bind single-stranded RNA in a sequence-specific and modular manner

CATH:  1.25.40.10
Gene Ontology:  GO:0003723
PubMed:  19004664|23635770|25882680|34065603|18031283|30809817
SCOP:  4001344

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 476-518 2.40e-08

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


:

Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 50.44  E-value: 2.40e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 12323218   476 WNSIIHAFCKSGRLGDAKSTFRRMTFLQYEPNNQTYLSLINGY 518
Cdd:pfam13041   6 YNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PLN03218 super family cl33664
maturation of RBCL 1; Provisional
 151-429 1.15e-05

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 48.72  E-value: 1.15e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12323218   151 LIDVCRENGSLAaflKVFrESCRIAVDEKLdfmKPDLVASNAALEACcRQMESLADAENLIESM--DVLGVKPDELSFGF 228
Cdd:PLN03218  513 LIDGCARAGQVA---KAF-GAYGIMRSKNV---KPDRVVFNALISAC-GQSGAVDRAFDVLAEMkaETHPIDPDHITVGA 584

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12323218   229 LAYLYARKGLREKISELEDLMDGLGFASRRILYSSMISGYVKSGDLDSAsdvilCSL------KGVGEASSFseetycel 302
Cdd:PLN03218  585 LMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFA-----LSIyddmkkKGVKPDEVF-------- 651

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12323218   303 vrgfiesksvesLAKLIieaqklesmstDVGGSVGFgivnacVKLGFSgksILDELNAQGGSGGIGVYVPILKAYCKEGR 382
Cdd:PLN03218  652 ------------FSALV-----------DVAGHAGD------LDKAFE---ILQDARKQGIKLGTVSYSSLMGACSNAKN 699

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 12323218   383 TSEATQLVTEISSSGLQLDVETYNTMIEASMTKHDFLSALTLFRDMR 429
Cdd:PLN03218  700 WKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMK 746
PLN03077 super family cl33629
Protein ECB2; Provisional
 470-575 3.42e-03

Protein ECB2; Provisional


The actual alignment was detected with superfamily member PLN03077:

Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 40.60  E-value: 3.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12323218  470 EVKSHDWNSIIHAFCKSGRLGDAKSTFRRMTFLQYEPNNQTYLSLINgyvSCE---KYFEVVVIWKEFKDKKAKLEHALA 546
Cdd:PLN03077  48 SSSTHDSNSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYVALFR---LCEwkrAVEEGSRVCSRALSSHPSLGVRLG 124

                         90       100
                 ....*....|....*....|....*....
gi 12323218  547 DAFLNALVKGGFFGTALQVIEKCQEMKIF 575
Cdd:PLN03077 125 NAMLSMFVRFGELVHAWYVFGKMPERDLF 153
 
Name Accession Description Interval E-value
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 476-518 2.40e-08

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 50.44  E-value: 2.40e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 12323218   476 WNSIIHAFCKSGRLGDAKSTFRRMTFLQYEPNNQTYLSLINGY 518
Cdd:pfam13041   6 YNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 151-429 1.15e-05

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 48.72  E-value: 1.15e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12323218   151 LIDVCRENGSLAaflKVFrESCRIAVDEKLdfmKPDLVASNAALEACcRQMESLADAENLIESM--DVLGVKPDELSFGF 228
Cdd:PLN03218  513 LIDGCARAGQVA---KAF-GAYGIMRSKNV---KPDRVVFNALISAC-GQSGAVDRAFDVLAEMkaETHPIDPDHITVGA 584

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12323218   229 LAYLYARKGLREKISELEDLMDGLGFASRRILYSSMISGYVKSGDLDSAsdvilCSL------KGVGEASSFseetycel 302
Cdd:PLN03218  585 LMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFA-----LSIyddmkkKGVKPDEVF-------- 651

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12323218   303 vrgfiesksvesLAKLIieaqklesmstDVGGSVGFgivnacVKLGFSgksILDELNAQGGSGGIGVYVPILKAYCKEGR 382
Cdd:PLN03218  652 ------------FSALV-----------DVAGHAGD------LDKAFE---ILQDARKQGIKLGTVSYSSLMGACSNAKN 699

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 12323218   383 TSEATQLVTEISSSGLQLDVETYNTMIEASMTKHDFLSALTLFRDMR 429
Cdd:PLN03218  700 WKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMK 746
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 373-411 1.18e-04

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 40.04  E-value: 1.18e-04
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 12323218   373 ILKAYCKEGRTSEATQLVTEISSSGLQLDVETYNTMIEA 411
Cdd:pfam13041   9 LINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILING 47
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 476-507 8.95e-04

pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 37.05  E-value: 8.95e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 12323218   476 WNSIIHAFCKSGRLGDAKSTFRRMTFLQYEPN 507
Cdd:TIGR00756   3 YNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PLN03077 PLN03077
Protein ECB2; Provisional
 470-575 3.42e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 40.60  E-value: 3.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12323218  470 EVKSHDWNSIIHAFCKSGRLGDAKSTFRRMTFLQYEPNNQTYLSLINgyvSCE---KYFEVVVIWKEFKDKKAKLEHALA 546
Cdd:PLN03077  48 SSSTHDSNSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYVALFR---LCEwkrAVEEGSRVCSRALSSHPSLGVRLG 124

                         90       100
                 ....*....|....*....|....*....
gi 12323218  547 DAFLNALVKGGFFGTALQVIEKCQEMKIF 575
Cdd:PLN03077 125 NAMLSMFVRFGELVHAWYVFGKMPERDLF 153
 
Name Accession Description Interval E-value
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 476-518 2.40e-08

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 50.44  E-value: 2.40e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 12323218   476 WNSIIHAFCKSGRLGDAKSTFRRMTFLQYEPNNQTYLSLINGY 518
Cdd:pfam13041   6 YNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 151-429 1.15e-05

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 48.72  E-value: 1.15e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12323218   151 LIDVCRENGSLAaflKVFrESCRIAVDEKLdfmKPDLVASNAALEACcRQMESLADAENLIESM--DVLGVKPDELSFGF 228
Cdd:PLN03218  513 LIDGCARAGQVA---KAF-GAYGIMRSKNV---KPDRVVFNALISAC-GQSGAVDRAFDVLAEMkaETHPIDPDHITVGA 584

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12323218   229 LAYLYARKGLREKISELEDLMDGLGFASRRILYSSMISGYVKSGDLDSAsdvilCSL------KGVGEASSFseetycel 302
Cdd:PLN03218  585 LMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFA-----LSIyddmkkKGVKPDEVF-------- 651

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12323218   303 vrgfiesksvesLAKLIieaqklesmstDVGGSVGFgivnacVKLGFSgksILDELNAQGGSGGIGVYVPILKAYCKEGR 382
Cdd:PLN03218  652 ------------FSALV-----------DVAGHAGD------LDKAFE---ILQDARKQGIKLGTVSYSSLMGACSNAKN 699

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 12323218   383 TSEATQLVTEISSSGLQLDVETYNTMIEASMTKHDFLSALTLFRDMR 429
Cdd:PLN03218  700 WKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMK 746
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 373-411 1.18e-04

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 40.04  E-value: 1.18e-04
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 12323218   373 ILKAYCKEGRTSEATQLVTEISSSGLQLDVETYNTMIEA 411
Cdd:pfam13041   9 LINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILING 47
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 476-500 6.39e-04

PPR repeat; This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known.


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 37.33  E-value: 6.39e-04
                          10        20
                  ....*....|....*....|....*
gi 12323218   476 WNSIIHAFCKSGRLGDAKSTFRRMT 500
Cdd:pfam12854  10 YNTLINGLCRAGRVDEAFELLDEME 34
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 476-507 8.95e-04

pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 37.05  E-value: 8.95e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 12323218   476 WNSIIHAFCKSGRLGDAKSTFRRMTFLQYEPN 507
Cdd:TIGR00756   3 YNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 476-499 1.81e-03

PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309 that may be involved in RNA stabilization. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein Swiss:O49549 that has a domain organization similar to the human BRCA1 protein. The repeat has been called PPR.


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 35.90  E-value: 1.81e-03
                          10        20
                  ....*....|....*....|....
gi 12323218   476 WNSIIHAFCKSGRLGDAKSTFRRM 499
Cdd:pfam01535   3 YNSLISGYCKNGKLEEALELFKEM 26
PLN03077 PLN03077
Protein ECB2; Provisional
 470-575 3.42e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 40.60  E-value: 3.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12323218  470 EVKSHDWNSIIHAFCKSGRLGDAKSTFRRMTFLQYEPNNQTYLSLINgyvSCE---KYFEVVVIWKEFKDKKAKLEHALA 546
Cdd:PLN03077  48 SSSTHDSNSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYVALFR---LCEwkrAVEEGSRVCSRALSSHPSLGVRLG 124

                         90       100
                 ....*....|....*....|....*....
gi 12323218  547 DAFLNALVKGGFFGTALQVIEKCQEMKIF 575
Cdd:PLN03077 125 NAMLSMFVRFGELVHAWYVFGKMPERDLF 153
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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